Ngari virus is a Bunyamwera virus reassortant that can be associated with large outbreaks of hemorrhagic fever in Africa

Abstract

Two isolates of a virus of the genus Orthobunyavirus (family Bunyaviridae) were obtained from hemorrhagic fever cases during a large disease outbreak in East Africa in 1997 and 1998. Sequence analysis of regions of the three genomic RNA segments of the virus (provisionally referred to as Garissa virus) suggested that it was a genetic reassortant virus with S and L segments derived from Bunyamwera virus but an M segment from an unidentified virus of the genus Orthobunyavirus. While high genetic diversity (52%) was revealed by analysis of virus M segment nucleotide sequences obtained from 21 members of the genus Orthobunyavirus, the Garissa and Ngari virus M segments were almost identical. Surprisingly, the Ngari virus L and S segments showed high sequence identity with those of Bunyamwera virus, showing that Garissa virus is an isolate of Ngari virus, which in turn is a Bunyamwera virus reassortant. Ngari virus should be considered when investigating hemorrhagic fever outbreaks throughout sub-Saharan Africa.

FIG. 1.

Phylogenetic relationships of Bunyamwera virus serogroup viruses. Virus RNA was extracted and purified, and RT-PCRs were carried out with primers M14C and M619R as described previously (6). In most cases, the RT-PCR product was sequenced directly; however, some products could not be sequenced directly because of mispriming. In those cases, the RT-PCR product was cloned into TOPO-TA (Invitrogen) and a minimum of three individual clones were sequenced with M13 forward and reverse primers (Invitrogen). Nucleotide sequences were aligned with PILEUP of the Wisconsin Package, version 10.2 (Accelerys, Inc.). Maximum-likelihood analysis of the 654-nucleotide aligned sequences of a region of the virus M segments was performed with PAUP4.0b10 (Sinauer Associates Inc., Sunderland, Mass.). The HKY85 substitution model was used and included empirical nucleotide frequencies, estimations of transition/transversion ratios, the proportion of invariable sites, and the gamma distribution shape parameter. The analysis took 2,148 h to run on a G4 Macintosh computer and resulted in a −Ln likelihood of 14848.26. Nucleotide sequences (accession numbers are in parentheses) from GenBank included those for Jatobal virus (AF312380), Oropouche virus (AF312381), Vinces virus (AF499012), Oriboca virus (AF499013), Cache Valley virus (AF186241, AF186242, AF186243, AF082576), Garissa virus (AF398345, AF398346), Bunyamwera virus (M11852), Germiston virus (M21951), Tahyna virus (AF23484, AF123485), Lumbo virus (AF229129), California encephalitis virus (AF123483), San Angelo virus (AF123486), La Crosse virus (U70205, U70206, U70207, U70208, U18979, U18980, D10370), snowshoe hare virus (K02539), Jerry Slough virus (AF123487), Jamestown Canyon virus (U88058), Inkoo virus (U88059, U88060), Jamestown Canyon-like virus (AF468197), South River virus (AF123488), Melao virus (U88057), Serra do Navio virus (AF123490), Keystone virus (AF123489), and Trivittatus virus (AF123491). The viruses analyzed in this study included the Anhembi virus (SpAr2984; GenBank accession no. AY593745), BeAr328208 virus (BeAr328208; AY593743), Birao virus (YMP-1; AY593748), Bozo virus (DakArB7343; AY593739), Fort Sherman virus (86-MSP18; AY593734), Iaco virus (BeAr314206; AY593746), Ilesha virus (RML2; AY593730), Lokern virus (FMS4332; AY593736), Macaua virus (BeAr306329; AY593742), Maguari virus (CBAAR426; AY593735), Mboke virus (DakArY357/6e; AY593731), Ngari virus (DakArD28542/4e; AY593747), Playas virus (75V3066; AY593733), Potosi virus (89-3380; AY593750), Shokwe virus (SAAr4042; AY593749), Sororoca virus (BeAr32149; AY593744), Taiassui virus (Ar671; AY593740), Tensaw virus (B479-490; AY593737), Tlacotalpan virus (61-D-240; AY593732), Wyeomyia virus (prototype; AY593741), and Xingu virus (BeH388464; AY593738).

FIG. 2.

Geographic distribution of Ngari and Bunyamwera viruses. Ngari virus has been isolated from animals and mosquitoes across a broad region of sub-Saharan Africa, including Senegal, Burkina Faso, Central African Republic, Madagascar, Mauritania, Kenya, and Somalia (black or hatched areas). This distribution overlaps that of Bunyamwera virus, which has been isolated from animals and mosquitoes in Senegal, Central African Republic, Madagascar, Guinea, Côte d'Ivoire, Uganda, Nigeria, Kenya South Africa, and Cameroon (gray or hatched areas). The countries in which both Bunyamwera virus and Ngari virus have been isolated are indicated by hatch marks. Only countries in which actual virus isolations were made are indicated. Antibody surveys suggest that the range of Bunyamwera virus is much of sub-Saharan Africa.